Coastal estuarine habitats are currently facing significant anthropogenic impacts, which have significantly influenced the biodiversity and ecosystem characteristics of benthic organisms. The aim of this study was to investigate the community structure and composition of polychaetes in the Vembanad estuarine system, which is the largest Ramsar site on the southwest coast of India. An artificial salinity barrier, the Thaneermukkom Barrage (TMB), was constructed in the estuarine ecosystem in 1975, resulting in a division of the system into a northern estuarine sector and a southern freshwater sector. By comparing the main ecological parameters of the Vembanad estuary before and after the construction of the barrage, it was evident that salinity experienced a drastic change. Spatially, the southern stations exhibited an oligohaline condition, while the northern stations displayed a mesohaline condition. Over three decades, there was a threefold increase in the amount of organic carbon in the sediment. A total of 19 polychaete species from 13 families and 19 genera were detected in the surface sediment samples from the ten selected stations. The time-scale study unveiled a significant shift in the distribution of polychaete species in the estuary. In the southern low salinity zone, only seven species of polychaetes were observed, most of which are considered classic indicators of disturbances and are responsive to organic enrichment. The decreasing salinity and increasing organic matter, particularly in the southern zone, may have contributed to a reduction in polychaete species diversity over the last 30 years. Based on the findings, the study suggests the need for effective policy formulation to manage the operation of TMB and control the discharge of waste from agriculture fields, houseboat tourism, and other developmental activities in the Vembanad estuarine system. Such measures are essential to safeguard the ecological integrity and biodiversity of this vital coastal ecosystem.